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Coexpression cluster:C938: Difference between revisions

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{{Coexpression_clusters
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transport!0.00428373742142871!11015;378;90411$GO:0015031!protein transport!0.00428373742142871!11015;378;90411$GO:0045184!establishment of protein localization!0.00428373742142871!11015;378;90411$GO:0008104!protein localization!0.00428373742142871!11015;378;90411$GO:0033036!macromolecule localization!0.00428373742142871!11015;378;90411$GO:0005737!cytoplasm!0.00733327368124839!11015;92689;3069;378;90411$GO:0006810!transport!0.00972679873071346!11015;3069;378;90411$GO:0051234!establishment of localization!0.00972679873071346!11015;3069;378;90411$GO:0046923!ER retention sequence binding!0.00972679873071346!11015$GO:0006621!protein retention in ER!0.0104499899438909!11015$GO:0051179!localization!0.0104499899438909!11015;3069;378;90411$GO:0005048!signal sequence binding!0.0213109713755608!11015$GO:0032507!maintenance of cellular protein localization!0.0213109713755608!11015$GO:0051651!maintenance of cellular localization!0.0213109713755608!11015$GO:0045185!maintenance of protein localization!0.0213109713755608!11015$GO:0005794!Golgi apparatus!0.0213109713755608!378;90411$GO:0051235!maintenance of localization!0.0298119136755056!11015$GO:0005793!ER-Golgi intermediate compartment!0.0298119136755056!90411$GO:0005783!endoplasmic reticulum!0.0301261191994913!11015;90411$GO:0044424!intracellular part!0.0342977698170602!11015;92689;3069;378;90411$GO:0008203!cholesterol metabolic 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|full_id=C938_leiomyoma_Smooth_Preadipocyte_hepatic_basal_Adipocyte_Ewing
|id=C938
}}

Latest revision as of 11:34, 17 September 2013


Full id: C938_leiomyoma_Smooth_Preadipocyte_hepatic_basal_Adipocyte_Ewing



Phase1 CAGE Peaks

Hg19::chr22:38864041..38864150,+p1@KDELR3
Hg19::chr2:242212239..242212257,-p1@HDLBP
Hg19::chr2:47142884..47142955,-p1@MCFD2
Hg19::chr3:57583064..57583079,-p1@ARF4
Hg19::chr3:57583085..57583121,-p2@ARF4
Hg19::chr3:57583130..57583152,-p3@ARF4
Hg19::chr4:38869366..38869387,+p3@FAM114A1
Hg19::chr4:38869393..38869404,+p2@FAM114A1
Hg19::chr4:38869410..38869435,+p1@FAM114A1


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0016192vesicle-mediated transport0.00428373742142871
GO:0015031protein transport0.00428373742142871
GO:0045184establishment of protein localization0.00428373742142871
GO:0008104protein localization0.00428373742142871
GO:0033036macromolecule localization0.00428373742142871
GO:0005737cytoplasm0.00733327368124839
GO:0006810transport0.00972679873071346
GO:0051234establishment of localization0.00972679873071346
GO:0046923ER retention sequence binding0.00972679873071346
GO:0006621protein retention in ER0.0104499899438909
GO:0051179localization0.0104499899438909
GO:0005048signal sequence binding0.0213109713755608
GO:0032507maintenance of cellular protein localization0.0213109713755608
GO:0051651maintenance of cellular localization0.0213109713755608
GO:0045185maintenance of protein localization0.0213109713755608
GO:0005794Golgi apparatus0.0213109713755608
GO:0051235maintenance of localization0.0298119136755056
GO:0005793ER-Golgi intermediate compartment0.0298119136755056
GO:0005783endoplasmic reticulum0.0301261191994913
GO:0044424intracellular part0.0342977698170602
GO:0008203cholesterol metabolic process0.0462566618772057



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
unilaminar epithelium7.81e-24148
trunk mesenchyme5.73e-23122
organism subdivision7.31e-23264
somite8.00e-2371
presomitic mesoderm8.00e-2371
presumptive segmental plate8.00e-2371
dermomyotome8.00e-2371
trunk paraxial mesoderm8.00e-2371
mesenchyme1.00e-22160
entire embryonic mesenchyme1.00e-22160
dense mesenchyme tissue1.19e-2273
epithelial vesicle1.36e-2278
multilaminar epithelium1.94e-2283
paraxial mesoderm4.31e-2272
presumptive paraxial mesoderm4.31e-2272
trunk1.99e-20199
skeletal muscle tissue2.77e-2062
striated muscle tissue2.77e-2062
myotome2.77e-2062
epithelial tube3.17e-20117
vasculature1.28e-1978
vascular system1.28e-1978
muscle tissue1.73e-1964
musculature1.73e-1964
musculature of body1.73e-1964
splanchnic layer of lateral plate mesoderm5.82e-1983
artery2.15e-1742
arterial blood vessel2.15e-1742
arterial system2.15e-1742
vessel4.36e-1768
epithelial tube open at both ends5.69e-1759
blood vessel5.69e-1759
blood vasculature5.69e-1759
vascular cord5.69e-1759
multi-cellular organism2.45e-15656
systemic artery1.20e-1433
systemic arterial system1.20e-1433
cardiovascular system1.99e-13109
cell layer4.74e-13309
circulatory system5.87e-13112
anatomical system6.01e-13624
anatomical group6.53e-13625
multi-tissue structure9.62e-13342
surface structure1.00e-1299
epithelium2.15e-12306
integument3.61e-0946
integumental system3.61e-0946
anatomical cluster4.44e-09373
mesoderm1.12e-08315
mesoderm-derived structure1.12e-08315
presumptive mesoderm1.12e-08315
anatomical conduit1.86e-08240
skin of body5.42e-0841
aorta6.63e-0821
aortic system6.63e-0821
embryonic structure6.37e-07564
organ component layer8.41e-0766
developing anatomical structure8.41e-07581
Disease
Ontology termp-valuen
ovarian cancer2.36e-0714


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.14.50329
MA0004.10.415381
MA0006.11.34805
MA0007.10.397529
MA0009.10.870971
MA0014.12.77991
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.11.40203
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.12.02319
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.42489
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.323879
MA0060.10.9464
MA0061.10.851955
MA0063.10
MA0066.11.28137
MA0067.11.18766
MA0068.11.18425
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.11.74484
MA0074.12.19307
MA0076.11.61616
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.12.03788
MA0084.11.37471
MA0087.10.838229
MA0088.11.92658
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.73976
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.12.10501
MA0103.10.257174
MA0105.12.36395
MA0106.10.554855
MA0107.11.11943
MA0108.21.68573
MA0109.10
MA0111.10.959847
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.11.31371
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.11.53859
MA0146.10.51271
MA0147.11.14329
MA0148.10.439278
MA0149.10.464973
MA0062.21.95022
MA0035.20.473658
MA0039.21.7915
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.22.15714
MA0047.20.542971
MA0112.20.674448
MA0065.20.0483532
MA0150.12.48541
MA0151.10
MA0152.11.20819
MA0153.10.969315
MA0154.10.842081
MA0155.10.0402662
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.12.79665
MA0163.10.873334
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.28.0379
MA0102.21.41188
MA0258.10.180288
MA0259.11.17199
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#46737.487724842002920.006050357420552810.0268411043515893
BATF#1053838.119267264101210.004821448895817150.0226242216484812
BRCA1#67236.728076881074590.008149333567200950.0321804389150371
CCNT2#90585.632179179522342.97597445628313e-060.000101075706094229
CHD2#110644.597343481829710.007379358397557620.0304971236469677
CTCFL#14069036.582158119658120.008659511962914930.032961249722825
E2F1#186984.36212374655942.18983367577486e-050.000481380844589036
E2F4#187445.630249029015310.003536571815964610.0179473286631452
E2F6#187673.902232235764630.0003067423599492730.00316341121069835
EGR1#195873.8796948515190.0003186557858542290.00326275408027744
ELK4#200547.215858514874680.001409539058987380.00916573375142164
ETS1#211377.566814050601823.61164439627206e-060.000118689908465153
GABPB1#255353.926491020101210.004337976092287310.0205868080657243
HEY1#2346294.040111043105713.4850025352467e-060.000116024921829337
HMGN3#932476.361092673717131.17234969197953e-050.000298122789093379
MAFF#23764318.77178549664840.0004336934263990230.00404921399603858
MAFK#797539.033577712609970.003567854712813750.0180841144553048
MEF2A#420536.247743636548020.01000005008462560.0374993799428462
NFYB#480135.586597751178820.01358500277111940.0479536318117056
NRF1#489945.426790865649290.004046698912068520.0193672984913172
POLR2A#543092.147453176558070.001029412892608020.00728936559028337
REST#597844.288901651612450.009457025945962830.0356692789010622
RFX5#599345.354627034308930.004249445027674740.0202217974778021
SIX5#14791235.6955717851530.01288794699034820.0463563953617915
SRF#672269.19811884144521.00386889165062e-050.000263094261418065
TAF1#687293.343046285745291.91655056102793e-050.000433627868377809
TFAP2C#702244.804101604382320.006299303434747120.0277885090357573
THAP1#55145310.45638153428380.002353923504026620.0133413695575534
ZBTB7A#5134154.084394059931050.003634990312833990.0183753510785126
ZEB1#693535.629477339181290.01330488236341950.047039560228611



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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